”Thee” was the old english word for singular ”you”, and ”you” was a plural words. Like in most languages in the area, the plural form was used for polite, and the polite version simply ”ate” the singular form of the word.

In other words, it kind of sounds very right for him to ”lower” Nicodemus’ status in such a way as to go away from the polite form and call him a mere ”thee” even though he’s king.